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From: Georcki Ropon (groponp_at_gmail.com)
Date: Wed Nov 17 2021 - 20:57:10 CST

I understand prof that in your experience this is extremely easy. But I tried to do this with a python script based on MDAnalysis, but the serial atoms for example for A are fine because they start with 1 as in the TOP file, but for segment B in the PDB the numbering of A continues and but in the TOP it starts with 1, so that's where I have problems.

Could you please provide me with an example, to be able to do what you mention.

Geo.

> On Nov 17, 2021, at 21:52, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> this doesn't make much sense to me.
> the position restraint section in the input for gromacs has an extremely simple structure, so it could easily be generated with a simple script.
> of course that can be done in Tcl, but also with Python, Bourne shell, or other suitable script languages. You don't really need the original PDB files for that.
>
> On Wed, Nov 17, 2021 at 9:22 PM Georcki Ropon <groponp_at_gmail.com <mailto:groponp_at_gmail.com>> wrote:
> I am using topogromacs to make MDs in gromacs,
>
> but I have two proteins A and B, so the serials of each of them start with 1, and since topogromacs does not generate position restraint file, I want to do this, using the atom serials of my PDB, but the serials of the PDB and TOP are different , so I want to renumber them.
>
> Geo.
>
>> On Nov 17, 2021, at 21:19, Axel Kohlmeyer <akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>> wrote:
>>
>> renumber what where and for what purpose?
>>
>> On Wed, Nov 17, 2021 at 9:17 PM Georcki Ropon <groponp_at_gmail.com <mailto:groponp_at_gmail.com>> wrote:
>> There is pathway to renumber it, with tcl?
>>
>>
>> Best,
>>
>> Geo.
>>
>>> On Nov 17, 2021, at 21:14, Axel Kohlmeyer <akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>> wrote:
>>>
>>> You cannot change the "serial" property. It is "index + 1" and both are read-only.
>>>
>>> On Wed, Nov 17, 2021 at 8:37 PM Georcki Ropon <groponp_at_gmail.com <mailto:groponp_at_gmail.com>> wrote:
>>> Dear user,
>>>
>>> I want change serial atom number , my number start with 3000 but I want all number (para chain B) start 1 2 3 4 ….
>>>
>>> Bellow my code but not fix it.
>>>
>>> mol new prot_orient_add_ter.pdb
>>>
>>> set prob [atomselect top "segid PROB"]
>>>
>>> set serials [$prob get serial]
>>>
>>> set count 0
>>> foreach atom $serials {
>>> $prob set serial $count
>>> incr $count
>>>
>>> }
>>>
>>> set all [atomselect top all]
>>> $all writepdb renum.pdb
>>> quit
>>>
>>>
>>> --
>>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uZUqH1mssXDMVXiXBDp11E1Rksnvdhv43sriyDht8NwsAMpkj8WqAbOyMZGHKHM0gA$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uZUqH1mssXDMVXiXBDp11E1Rksnvdhv43sriyDht8NwsAMpkj8WqAbOyMZGHKHM0gA$ >
>>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uZUqH1mssXDMVXiXBDp11E1Rksnvdhv43sriyDht8NwsAMpkj8WqAbOyMZGHKHM0gA$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uZUqH1mssXDMVXiXBDp11E1Rksnvdhv43sriyDht8NwsAMpkj8WqAbOyMZGHKHM0gA$ >
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com> https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uZUqH1mssXDMVXiXBDp11E1Rksnvdhv43sriyDht8NwsAMpkj8WqAbOyMZGHKHM0gA$ <https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!uZUqH1mssXDMVXiXBDp11E1Rksnvdhv43sriyDht8NwsAMpkj8WqAbOyMZGHKHM0gA$ >
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.